When separating panels you will want to clean the area where the seams are spot welded so that you can see where drilling needs to be done. Center punch each spot where you will be drilling then, using a variable speed drill and a spot weld bit (shown) drill out the weld.

You want to rotate the bit slowly so that it doesn't get hot and dull the bit AND place a drop of oil on the place before or during the cutting. Drill through the first layer of metal with the cutter but NOT through both layers. If the bit did not reach all of the weld you may need to pry the layers of metal apart but try not to distort the panel that will remain on the car. The picture below shows how the pilot bit is the only hole in the remaining panel.